{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}, "pi": {"error": "no view permissions"}}, "award": {"project": "4DN", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "center_title": "DCIC - DCIC", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "status": "current", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators with a strong track record in analysis of chromatin interaction data, image processing and three-dimensional data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and flexible cloud technologies. In Aim 1, we will develop efficient submission pipelines for data and metadata from 4DN data production groups. We will define data/metadata requirements and quality metrics in conjunction with the production groups and ensure that high-quality, well- annotated data become available to the wider scientific community in a timely manner. In Aim 2, we will develop a user-friendly data portal for the broad scientific community. This portal will provide an easy-to-navigate interface for accessing raw and intermediate data files, allow for programmatic access via APIs, and will incorporate novel analysis and visualization tools developed by DCIC as well as other Network members. For computing and storage scalability and cost-effectiveness, significant efforts will be devoted to development and deployment of cloud-based technology. We will conduct tutorials and workshops to facilitate the use of 4DN data and tools by external investigators. In Aim 3, we will coordinate and assist in conducting integrative analysis of the multiple data types. These efforts will examine key questions in higher-order chromatin organization using both sequence and image data, and the tools and algorithms developed here will be incorporated into the data portal for use by other investigators. These three aims will ensure that the data generated in 4DN will have maximal impact for the scientific community.", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "name": "1U01CA200059-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "2928d5ee4363af8937536194adef9c7b", "status": "released", "accession": "4DNFI7NWWWNA", "file_size": 7015673874, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFI7NWWWNA/@@download/4DNFI7NWWWNA.pairs.gz.px2", "uuid": "e28cf559-a225-4eaa-b263-7c750bf7f598", "md5sum": "e12ce742464331f0266308645b4a1af4", "status": "released", "filename": "4DNFI7NWWWNA", "accession": "4DNFI7NWWWNA", "file_size": 29319933, "upload_key": "e28cf559-a225-4eaa-b263-7c750bf7f598/4DNFI7NWWWNA.pairs.gz.px2", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"status": "released", "file_format": "pairs", "display_title": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2019-05-19T23:13:47.314955+00:00", "notes_to_tsv": ["WARNING: some distinct reads in this file may share the same identifier because the file was generated after merging fastq files with integer identifiers (eg. @1, @2) during processing."], "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-04-06T20:33:49.076429+00:00"}, "public_release": "2019-11-26", "quality_metric": {"Cis reads (>20kb)": 212742137, "@id": "/quality-metrics-pairsqc/afd98383-bfb4-4040-af17-2c53752de757/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7NWWWNA/pairsqc_report.html", "Trans reads": 174272828, "uuid": "afd98383-bfb4-4040-af17-2c53752de757", "Total reads": 460542259, "display_title": "QualityMetricPairsqc from 2019-05-23", "Short cis reads (<20kb)": 73527294, "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "460542259", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "46.194", "tooltip": "Percent of filtered reads (=212.74m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "15.965", "tooltip": "Percent of filtered reads (=73.53m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "37.841", "tooltip": "Percent of filtered reads (=174.27m)", "numberType": "percent"}]}, "schema_version": "3", "static_headers": [], "genome_assembly": "GRCh38", "project_release": "2019-11-26", "contributing_labs": [{"@id": "/labs/erez-liebermanaiden-lab/", "display_title": "Erez Lieberman Aiden, BCM", "uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "ZXJlekBlcmV6LmNvbQ==", "@id": "/users/60938b2e-e120-4c4f-9ddb-001296021df7/", "display_title": "Erez Lieberman Aiden"}], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5771d772-1d10-43ea-bec1-0ea8c5a58503"]}}], "source_experiments": ["9fcea9ba-ad0c-497c-bf0e-6f8860da3352"], "file_classification": "processed file", "@id": "/files-processed/4DNFI7NWWWNA/", "@type": ["FileProcessed", "File", "Item"], "uuid": "e28cf559-a225-4eaa-b263-7c750bf7f598", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI7NWWWNA.pairs.gz", "external_references": [], "experiments": [{"@id": "/experiments-hi-c/4DNEXMSLJGGQ/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "9fcea9ba-ad0c-497c-bf0e-6f8860da3352", "accession": "4DNEXMSLJGGQ", "display_title": "in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI - 4DNEXMSLJGGQ", "status": "released", "biosample": {"biosource_summary": "HCT116 with Crispr generated mClover and AID-tagged RAD21", "modifications_summary": "None", "treatments_summary": "IAA treatment (500.0 \u03bcM, 6.0h)", "accession": "4DNBSSN9GYTY", "display_title": "4DNBSSN9GYTY", "status": "released", "@type": ["Biosample", "Item"], "uuid": "ecfd5c90-9388-43f3-a71f-64582ceccf67", "@id": "/biosamples/4DNBSSN9GYTY/", "biosource": [{"display_title": "HCT116 with Crispr generated mClover and AID-tagged RAD21 - 4DNSRG1Q4WCR", "@id": "/biosources/4DNSRG1Q4WCR/", "uuid": "2b46c4e3-780f-40bc-929f-f1c1a2e181f1", "biosource_type": "immortalized cell line", "status": "released", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "modifications": [{"uuid": "1cc89862-1db3-48d0-8d1e-2f954f133e2e", "@type": ["Modification", "Item"], "genomic_change": "insertion", "modification_type": "Crispr", "display_title": "Crispr generated mClover and AID-tagged RAD21", "status": "released", "override_modification_name": "Crispr generated mClover and AID-tagged RAD21", "@id": "/modifications/1cc89862-1db3-48d0-8d1e-2f954f133e2e/", "target_of_mod": [{"organism_name": "human", "@type": ["BioFeature", "Item"], "@id": "/bio-features/c3ce0816-5481-4342-b95b-6c8b93199744/", "display_title": "RAD21 gene", "status": "released", "uuid": "c3ce0816-5481-4342-b95b-6c8b93199744", "feature_type": {"status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "gene", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@id": "/ontology-terms/SO:0000704/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relevant_genes": [{"@type": ["Gene", "Item"], "display_title": "RAD21", "uuid": "a093769c-d596-4a26-8916-06ae491575ba", "@id": "/genes/5885/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_line": {"term_id": "EFO:0002824", "preferred_name": "HCT116", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "@id": "/ontology-terms/EFO:0002824/", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "HCT116", "display_title": "HCT116", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"name": "human", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-human/4DNINJ6WV6L1/", "status": "released", "protected_data": false, "display_title": "4DNINJ6WV6L1", "uuid": "1f0f0999-c5b4-430e-8650-8ebb3491d699", "@type": ["IndividualHuman", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_name": "colon", "term_id": "UBERON:0001155", "status": "released", "@id": "/ontology-terms/UBERON:0001155/", "preferred_name": "colon", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "display_title": "colon", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESJV9TH8Q/", "uuid": "1a99264a-e679-488c-9150-645cc2ef1148", "experimentset_type": "replicate", "display_title": "4DNESJV9TH8Q", "accession": "4DNESJV9TH8Q", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"@type": ["ExperimentType", "Item"], "@id": "/experiment-types/in-situ-hi-c/", "status": "released", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "display_title": "in situ Hi-C", "title": "in situ Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-07-08T14:25:08.641281+00:00"}, "digestion_enzyme": {"name": "MboI", "@type": ["Enzyme", "Item"], "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "status": "released", "display_title": "MboI", "@id": "/enzymes/MboI/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "contact list-replicate (pairs)", "track_and_facet_info": {"experimental_lab": "Erez Lieberman Aiden, BCM", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "Hi-C on RAD21-AID tagged HCT-116", "condition": "6h auxin treatment", "replicate_info": "Biorep 1, Techrep 3", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged RAD21", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFI7NWWWNA", "href": "/files-processed/4DNFI7NWWWNA/@@download/4DNFI7NWWWNA.pairs.gz", "upload_key": "e28cf559-a225-4eaa-b263-7c750bf7f598/4DNFI7NWWWNA.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e28cf559-a225-4eaa-b263-7c750bf7f598/4DNFI7NWWWNA.pairs.gz", "tsv_notes": "WARNING: some distinct reads in this file may share the same identifier because the file was generated after merging fastq files with integer identifiers (eg. @1, @2) during processing.", "workflow_run_inputs": [{"display_title": "pairsqc-single 0.2.6 run 2019-05-23 03:33:20.412577", "@id": "/workflow-runs-awsem/ff0f88a6-280e-4c8f-971e-fbfa01a47444/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "ff0f88a6-280e-4c8f-971e-fbfa01a47444", "output_files": [{"workflow_argument_name": "report", "value_qc": {"display_title": "QualityMetricPairsqc from 2019-05-23", "@id": "/quality-metrics-pairsqc/afd98383-bfb4-4040-af17-2c53752de757/", "overall_quality_status": "PASS", "status": "released", "uuid": "afd98383-bfb4-4040-af17-2c53752de757", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7NWWWNA/pairsqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "PairsQC 0.2.6 - 4DNWFHB26CID", "@id": "/workflows/4DNWFHB26CID/", "status": "released", "title": "PairsQC 0.2.6", "@type": ["Workflow", "Item"], "uuid": "b8c533e0-f8c0-4510-b4a1-ac35158e27c3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"display_title": "4DNFI823LSII.chrom.sizes", "@type": ["FileReference", "File", "Item"], "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "accession": "4DNFI823LSII", "filename": "hg38.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI823LSII/", "status": "released", "file_format": {"display_title": "chromsizes", "file_format": "chromsizes", "@id": "/file-formats/chromsizes/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFI7NWWWNA.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "e28cf559-a225-4eaa-b263-7c750bf7f598", "accession": "4DNFI7NWWWNA", "@id": "/files-processed/4DNFI7NWWWNA/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "hi-c-processing-pairs 0.2.7 run 2019-05-23 14:27:43.616630", "@id": "/workflow-runs-awsem/700d6433-8186-48ff-a40a-d1f366fc71f1/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "700d6433-8186-48ff-a40a-d1f366fc71f1", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"accession": "4DNFI2X45Z5L", "@type": ["FileProcessed", "File", "Item"], "uuid": "af6d2d63-bb71-452c-b62b-6a7ab825672f", "display_title": "4DNFI2X45Z5L.pairs.gz", "status": "released", "@id": "/files-processed/4DNFI2X45Z5L/", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "hic", "value": {"accession": "4DNFILIM6FDL", "@type": ["FileProcessed", "File", "Item"], "uuid": "8ac79b4f-cfbf-4b2a-9fc2-898ed6c3e5e1", "display_title": "4DNFILIM6FDL.hic", "status": "released", "@id": "/files-processed/4DNFILIM6FDL/", "file_format": {"status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "file_format": "hic", "display_title": "hic", "@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"accession": "4DNFILP99QJS", "@type": ["FileProcessed", "File", "Item"], "uuid": "d62ac53a-4bfc-4184-ad26-762477de727b", "display_title": "4DNFILP99QJS.mcool", "status": "released", "@id": "/files-processed/4DNFILP99QJS/", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "file_format": "mcool", "display_title": "mcool", "@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7 - 4DNWF2YBHXQM", "@id": "/workflows/4DNWF2YBHXQM/", "status": "released", "title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7", "@type": ["Workflow", "Item"], "uuid": "23bd6d73-4190-496d-837c-21bcdb3802ed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"display_title": "4DNFI823LSII.chrom.sizes", "@type": ["FileReference", "File", "Item"], "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "accession": "4DNFI823LSII", "filename": "hg38.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI823LSII/", "status": "released", "file_format": {"display_title": "chromsizes", "file_format": "chromsizes", "@id": "/file-formats/chromsizes/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIR7Q949M.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "0d153a4b-2d8e-48a4-9871-ee52cda54b64", "accession": "4DNFIR7Q949M", "@id": "/files-processed/4DNFIR7Q949M/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIQA9LNI9.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "f4ce13ef-69f3-4a41-82f0-3f7149a32d33", "accession": "4DNFIQA9LNI9", "@id": "/files-processed/4DNFIQA9LNI9/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFI7NWWWNA.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "e28cf559-a225-4eaa-b263-7c750bf7f598", "accession": "4DNFI7NWWWNA", "@id": "/files-processed/4DNFI7NWWWNA/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFI5HOVNFS.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "4d84302f-5e02-4bac-90f2-3c065da738cb", "accession": "4DNFI5HOVNFS", "@id": "/files-processed/4DNFI5HOVNFS/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFICOPDAE8.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "bf8568b9-b63f-4698-b9b7-07266fa45297", "accession": "4DNFICOPDAE8", "@id": "/files-processed/4DNFICOPDAE8/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIIMOHDU7.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "4b5960d7-8063-4493-9486-0339e1cc5845", "accession": "4DNFIIMOHDU7", "@id": "/files-processed/4DNFIIMOHDU7/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIL7KMTWP.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "c3078fc7-48e0-4016-92ad-7045d0eacfc6", "accession": "4DNFIL7KMTWP", "@id": "/files-processed/4DNFIL7KMTWP/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIY54E2P3.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "99e12212-1640-462d-be9d-97259d904b0d", "accession": "4DNFIY54E2P3", "@id": "/files-processed/4DNFIY54E2P3/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIH4SJBET.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "997e17c9-5fb6-48bf-a74c-5f0c46bfa8ea", "accession": "4DNFIH4SJBET", "@id": "/files-processed/4DNFIH4SJBET/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIQGDALKM.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "321434d0-6d76-4afb-ab9c-34e20fbc1348", "accession": "4DNFIQGDALKM", "@id": "/files-processed/4DNFIQGDALKM/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFI51KTR81.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "83d7d4fc-5db6-4446-ad1b-bfc029cb4240", "accession": "4DNFI51KTR81", "@id": "/files-processed/4DNFI51KTR81/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIUF93RY8.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "cf7eb1ea-e8a7-4994-9ce0-11325595938a", "accession": "4DNFIUF93RY8", "@id": "/files-processed/4DNFIUF93RY8/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIZKYZ8XC.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "6ecf179a-36e7-4058-b383-7acb4aaaa3ee", "accession": "4DNFIZKYZ8XC", "@id": "/files-processed/4DNFIZKYZ8XC/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIDWHN7T9.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "579179e9-b52b-4892-a758-09e3e14af338", "accession": "4DNFIDWHN7T9", "@id": "/files-processed/4DNFIDWHN7T9/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"display_title": "4DNFIOC7EA4B.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "5805f17a-b1e0-4528-b395-8fc9a5f36233", "accession": "4DNFIOC7EA4B", "@id": "/files-processed/4DNFIOC7EA4B/", "status": "released", "file_format": {"display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "restriction_file", "value": {"display_title": "4DNFI823L812.txt", "@type": ["FileReference", "File", "Item"], "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d582084", "accession": "4DNFI823L812", "filename": "hg38_MboI.txt", "@id": "/files-reference/4DNFI823L812/", "status": "released", "file_format": {"display_title": "juicer_format_restriction_site_file", "file_format": "juicer_format_restriction_site_file", "@id": "/file-formats/juicer_format_restriction_site_file/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "hi-c-processing-bam 0.2.6 run 2019-05-19 23:13:47.515771", "@id": "/workflow-runs-awsem/36427cc2-7d7c-4238-a880-093934f5c23a/", "uuid": "36427cc2-7d7c-4238-a880-093934f5c23a", "input_files": [{"workflow_argument_name": "chromsize", "value": {"accession": "4DNFI823LSII", "@id": "/files-reference/4DNFI823LSII/", "@type": ["FileReference", "File", "Item"], "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "display_title": "4DNFI823LSII.chrom.sizes", "filename": "hg38.mainonly.chrom.sizes", "status": "released", "file_format": {"file_format": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFI4TSTY4U", "@id": "/files-processed/4DNFI4TSTY4U/", "@type": ["FileProcessed", "File", "Item"], "uuid": "afcdd01c-9eaf-409f-9b36-c6715c4795be", "display_title": "4DNFI4TSTY4U.bam", "status": "released", "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFIJGA5UZH", "@id": "/files-processed/4DNFIJGA5UZH/", "@type": ["FileProcessed", "File", "Item"], "uuid": "1d58f5a4-f594-4c98-b00d-aca04a5e9828", "display_title": "4DNFIJGA5UZH.bam", "status": "released", "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFI48V6P6I", "@id": "/files-processed/4DNFI48V6P6I/", "@type": ["FileProcessed", "File", "Item"], "uuid": "e6fbc399-2a85-454f-98c7-f03357105bb0", "display_title": "4DNFI48V6P6I.bam", "status": "released", "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFIK4B6LRM", "@id": "/files-processed/4DNFIK4B6LRM/", "@type": ["FileProcessed", "File", "Item"], "uuid": "c9a35a19-6b7a-431b-a96c-2108bc86f8b4", "display_title": "4DNFIK4B6LRM.bam", "status": "released", "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFIR3UNLL8", "@id": "/files-processed/4DNFIR3UNLL8/", "@type": ["FileProcessed", "File", "Item"], "uuid": "d546c712-d204-423c-90dd-1c57bc4fcbb0", "display_title": "4DNFIR3UNLL8.bam", "status": "released", "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFIJ42GBOB", "@id": "/files-processed/4DNFIJ42GBOB/", "@type": ["FileProcessed", "File", "Item"], "uuid": "afc29937-9460-4723-90cf-137e0efdb8af", "display_title": "4DNFIJ42GBOB.bam", "status": "released", "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"@id": "/files-processed/4DNFIMO766R4/", "@type": ["FileProcessed", "File", "Item"], "uuid": "960b5f8c-7fa5-4722-8322-264112001ea5", "status": "released", "display_title": "4DNFIMO766R4.bam", "accession": "4DNFIMO766R4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "filtered_pairs", "value": {"@id": "/files-processed/4DNFI7NWWWNA/", "@type": ["FileProcessed", "File", "Item"], "uuid": "e28cf559-a225-4eaa-b263-7c750bf7f598", "status": "released", "display_title": "4DNFI7NWWWNA.pairs.gz", "accession": "4DNFI7NWWWNA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"@id": "/workflows/4DNWFT69RBY4/", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "@type": ["Workflow", "Item"], "status": "released", "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "title": "Hi-C Post-alignment Processing 0.2.6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "pairsqc_table": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7NWWWNA/4DNFI7NWWWNA.plot_table.out", "source_experiment_sets": [{"status": "released", "display_title": "4DNESJV9TH8Q", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "1a99264a-e679-488c-9150-645cc2ef1148", "@id": "/experiment-set-replicates/4DNESJV9TH8Q/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXMSLJGGQ/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2024-07-08T14:25:08.641281+00:00"}}, {"parent": "/files-processed/4DNFI7NWWWNA/", "embedded_path": "last_modified", "item": {"date_modified": "2021-04-06T20:33:49.076429+00:00"}}]}, "validation-errors": []}